tbuckley/cabot-search huggingface dataset:
Erratum
Journal: Hepatology (2022)

HepatologyEarly View ERRATUMFree Access Erratum This article corrects the following: Transcriptome Profiling Identifies TIGIT as a Marker of T-Cell Exhaustion in Liver Cancer Dmitrij Ostroumov, Steven Duong, Jessica Wingerath, Norman Woller, Michael P. Manns, Kai Timrott, Moritz Kleine, Wolf Ramackers, Stephanie Roessler, Sven Nahnsen, Stefan Czemmel, Oliver Dittrich-Breiholz, Tobias Eggert, Florian Kühnel, Thomas C. Wirth, Volume 73Issue 4Hepatology pages: 1399-1418 First Published online: April 13, 2021 First published: 13 May 2022 https://doi.org/10.1002/hep.32561AboutSectionsPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat In the article by Ostroumov et al.,[1] an error appeared in author Stefan Czemmel’s name and has since been corrected. We apologize for this error. REFERENCE 1Ostroumov D, Duong S, Wingerath J, Woller N, Manns MP, Timrott K, et al. Transcriptome profiling identifies TIGIT as a marker of T-cell exhaustion in liver cancer. Hepatology. 2021; 73: 1399– 418. https://doi.org/10.1002/hep.31466Wiley Online LibraryCASPubMedWeb of Science®Google Scholar Early ViewOnline Version of Record before inclusion in an issue ReferencesRelatedInformation
AI recognition of patient race in medical imaging: a modelling study
Authors: Judy Wawira Gichoya, Imon Banerjee, Ananth Reddy Bhimireddy, John L Burns, Leo Anthony Celi, Li-Ching Chen, Ramon Correa, Natalie Dullerud, Marzyeh Ghassemi, Shih-Cheng Huang, Po-Chih Kuo, Matthew P Lungren, Lyle J Palmer, Brandon J Price, Saptarshi Purkayastha, Ayis T Pyrros, Lauren Oakden-Rayner, Chima Okechukwu, Laleh Seyyed-Kalantari, Hari Trivedi, Ryan Wang, Zachary Zaiman, Haoran Zhang
Journal: The Lancet Digital Health (2022)

Background: In medical imaging, prior studies have demonstrated disparate AI performance by race, yet there is no known correlation for race on medical imaging that would be obvious to the human expert interpreting the images. Methods: Using private and public datasets we evaluate: A) performance quantification of deep learning models to detect race from medical images, including the ability of these models to generalize to external environments and across multiple imaging modalities, B) assessment of possible confounding anatomic and phenotype population features, such as disease distribution and body habitus as predictors of race, and C) investigation into the underlying mechanism by which AI models can recognize race. Findings: Standard deep learning models can be trained to predict race from medical images with high performance across multiple imaging modalities. Our findings hold under external validation conditions, as well as when models are optimized to perform clinically motivated tasks. We demonstrate this detection is not due to trivial proxies or imaging-related surrogate covariates for race, such as underlying disease distribution. Finally, we show that performance persists over all anatomical regions and frequency spectrum of the images suggesting that mitigation efforts will be challenging and demand further study. Interpretation: We emphasize that model ability to predict self-reported race is itself not the issue of importance. However, our findings that AI can trivially predict self-reported race -- even from corrupted, cropped, and noised medical images -- in a setting where clinical experts cannot, creates an enormous risk for all model deployments in medical imaging: if an AI model secretly used its knowledge of self-reported race to misclassify all Black patients, radiologists would not be able to tell using the same data the model has access to.
Risk of Infection and Hospitalization Among Vaccinated and Unvaccinated Children and Adolescents in New York After the Emergence of the Omicron Variant
Authors: Vajeera Dorabawila, Dina Hoefer, Ursula E. Bauer, Mary T. Bassett, Emily Lutterloh, Eli S. Rosenberg
Journal: JAMA (2022)

Katherine E. Fleming-Dutra, MD; Amadea Britton, MD; Nong Shang, PhD; Gordana Derado, PhD; Ruth Link-Gelles, PhD; Emma K. Accorsi, PhD; Zachary R. Smith, MA; Joseph Miller, PhD; Jennifer R. Verani, MD; Stephanie J. Schrag, DPhil
Durable immunogenicity, adaptation to emerging variants, and low-dose efficacy of an AAV-based COVID-19 vaccine platform in macaques
Authors: Nerea Zabaleta, Urja Bhatt, Cécile Hérate, Pauline Maisonnasse, Julio Sanmiguel, Cheikh Diop, Sofia Castore, Reynette Estelien, Dan Li, Nathalie Dereuddre-Bosquet, Mariangela Cavarelli, Anne-Sophie Gallouët, Quentin Pascal, Thibaut Naninck, Nidhal Kahlaoui, Julien Lemaitre, Francis Relouzat, Giuseppe Ronzitti, Hendrik Jan Thibaut, Emanuele Montomoli, James M. Wilson, Roger Le Grand, Luk H. Vandenberghe
Journal: Molecular Therapy (2022)

The COVID-19 pandemic continues to have devastating consequences on health and economy, even after the approval of safe and effective vaccines. Waning immunity, the emergence of variants of concern, breakthrough infections, and lack of global vaccine access and acceptance perpetuate the epidemic. Here, we demonstrate that a single injection of an adenoassociated virus (AAV)-based COVID-19 vaccine elicits at least 17-month-long neutralizing antibody responses in non-human primates at levels that were previously shown to protect from viral challenge. To improve the scalability of this durable vaccine candidate, we further optimized the vector design for greater potency at a reduced dose in mice and non-human primates. Finally, we show that the platform can be rapidly adapted to other variants of concern to robustly maintain immunogenicity and protect from challenge. In summary, we demonstrate this class of AAV can provide durable immunogenicity, provide protection at dose that is low and scalable, and be adapted readily to novel emerging vaccine antigens thus may provide a potent tool in the ongoing fight against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2).
Analysis of Antiemetic Use After Initiation of Hormone Therapy
Authors: Martin Torp Rahbek, Erika Angelica Björkström Gram, Jesper Hallas, Mette Marie Hougaard Christensen, Lars Christian Lund
Journal: JAMA Network Open (2022)

Our results suggest that HT-related nausea may be treated with antiemetics instead of dose reduction or discontinuation.This prescribing cascade is an unintended outcome associated with HT, which our results suggest may be avoided.
Interactome of Aiolos/Ikaros Reveals Combination Rationale of Cereblon Modulators with HDAC Inhibitors in DLBCL
Authors: Patrick R. Hagner, Hsiling Chiu, Vivek S. Chopra, Martino Colombo, Nisha Patel, Maria Ortiz Estevez, Michelle F. Waldman, Remco Loos, Fadi Towfic, Anita K. Gandhi
Journal: Clinical Cancer Research (2022)

Abstract Purpose: Cereblon (CRBN), a substrate receptor of the E3 ubiquitin ligase complex CRL4CRBN, is the target of the small molecules lenalidomide and avadomide. Upon binding of the drugs, Aiolos and Ikaros are recruited to the E3 ligase, ubiquitylated, and subsequently degraded. In diffuse large B-cell lymphoma (DLBCL) cells, Aiolos and Ikaros are direct transcriptional repressors of interferon-stimulated genes (ISG) and degradation of these substrates results in increased ISG protein levels resulting in decreased proliferation and apoptosis. Herein, we aimed to uncover the mechanism(s) Aiolos and Ikaros use to repress ISG transcription and provide a mechanistic rationale for a combination strategy to enhance cell autonomous activities of CRBN modulators (CELMoD). Experimental Design: We conducted paired RNA sequencing with histone modification and Aiolos/Ikaros chromatin immunoprecipitation sequencing to identify genes regulated by these transcription factors and to elucidate correlations to drug sensitivity. We confirmed Aiolos/Ikaros mediated transcriptional complex formation in DLBCL patient samples including those treated with avadomide. Results: In DLBCL, the repression of ISG transcription is accomplished in part through recruitment of large transcriptional complexes such as the nucleosome remodeling and deacetylase, which modify the chromatin landscape of these promoters. A rational combination approach of avadomide with a specific histone deacetylase inhibitor leads to a significant increase in ISG transcription compared with either single agent, and synergistic antiproliferative activity in DLBCL cell lines. Conclusions: Our results provide a novel role for lineage factors Aiolos and Ikaros in DLBCL as well as further insight into the mechanism(s) of Aiolos and Ikaros–mediated transcriptional repression and unique therapeutic combination strategies.
3D cell-printing of gradient multi-tissue interfaces for rotator cuff regeneration
Authors: Suhun Chae, Uijung Yong, Wonbin Park, Yoo-mi Choi, In-Ho Jeon, Homan Kang, Jinah Jang, Hak Soo Choi, Dong-Woo Cho
Journal: Bioactive Materials (2022)

Owing to the prevalence of rotator cuff (RC) injuries and suboptimal healing outcome, rapid and functional regeneration of the tendon-bone interface (TBI) after RC repair continues to be a major clinical challenge. Given the essential role of the RC in shoulder movement, the engineering of biomimetic multi-tissue constructs presents an opportunity for complex TBI reconstruction after RC repair. Here, we propose a gradient cell-laden multi-tissue construct combined with compositional gradient TBI-specific bioinks via 3D cell-printing technology. In vitro studies demonstrated the capability of a gradient scaffold system in zone-specific inducibility and multi-tissue formation mimicking TBI. The regenerative performance of the gradient scaffold on RC regeneration was determined using a rat RC repair model. In particular, we adopted nondestructive, consecutive, and tissue-targeted near-infrared fluorescence imaging to visualize the direct anatomical change and the intricate RC regeneration progression in real time in vivo. Furthermore, the 3D cell-printed implant promotes effective restoration of shoulder locomotion function and accelerates TBI healing in vivo. In summary, this study identifies the therapeutic contribution of cell-printed constructs towards functional RC regeneration, demonstrating the translational potential of biomimetic gradient constructs for the clinical repair of multi-tissue interfaces.
Visualising harms in publications of randomised controlled trials: consensus and recommendations
Authors: Rachel Phillips, Suzie Cro, Graham Wheeler, Simon Bond, Tim P Morris, Siobhan Creanor, Catherine Hewitt, Sharon Love, Andre Lopes, Iryna Schlackow, Carrol Gamble, Graeme MacLennan, Chris Habron, Anthony C Gordon, Nikhil Vergis, Tianjing Li, Riaz Qureshi, Colin C Everett, Jane Holmes, Amanda Kirkham, Clare Peckitt, Sarah Pirrie, Norin Ahmed, Laura Collett, Victoria Cornelius
Journal: BMJ (2022)

Abstract Objective To improve communication of harm in publications of randomised controlled trials via the development of recommendations for visually presenting harm outcomes. Design Consensus study. Setting 15 clinical trials units registered with the UK Clinical Research Collaboration, an academic population health department, Roche Products, and The BMJ . Participants Experts in clinical trials: 20 academic statisticians, one industry statistician, one academic health economist, one data graphics designer, and two clinicians. Main outcome measures A methodological review of statistical methods identified visualisations along with those recommended by consensus group members. Consensus on visual recommendations was achieved (at least 60% of the available votes) over a series of three meetings with participants. The participants reviewed and critically appraised candidate visualisations against an agreed framework and voted on whether to endorse each visualisation. Scores marginally below this threshold (50-60%) were revisited for further discussions and votes retaken until consensus was reached. Results 28 visualisations were considered, of which 10 are recommended for researchers to consider in publications of main research findings. The choice of visualisations to present will depend on outcome type (eg, binary, count, time-to-event, or continuous), and the scenario (eg, summarising multiple emerging events or one event of interest). A decision tree is presented to assist trialists in deciding which visualisations to use. Examples are provided of each endorsed visualisation, along with an example interpretation, potential limitations, and signposting to code for implementation across a range of standard statistical software. Clinician feedback was incorporated into the explanatory information provided in the recommendations to aid understanding and interpretation. Conclusions Visualisations provide a powerful tool to communicate harms in clinical trials, offering an alternative perspective to the traditional frequency tables. Increasing the use of visualisations for harm outcomes in clinical trial manuscripts and reports will provide clearer presentation of information and enable more informative interpretations. The limitations of each visualisation are discussed and examples of where their use would be inappropriate are given. Although the decision tree aids the choice of visualisation, the statistician and clinical trial team must ultimately decide the most appropriate visualisations for their data and objectives. Trialists should continue to examine crude numbers alongside visualisations to fully understand harm profiles.
Machine‐Assisted Discovery of Chondroitinase ABC Complexes toward Sustained Neural Regeneration (Adv. Healthcare Mater. 10/2022)
Authors: Shashank Kosuri, Carlos H. Borca, Heloise Mugnier, Matthew Tamasi, Roshan A. Patel, Isabel Perez, Suneel Kumar, Zachary Finkel, Rene Schloss, Li Cai, Martin L. Yarmush, Michael A. Webb, Adam J. Gormley
Journal: Advanced Healthcare Materials (2022)

Machine Learning In article number 2102101, using a combination of robotics and machine learning, Michael A. Webb, Adam J. Gormley, and co-workers design complex copolymers that thermostabilize chondroitinase ABC for sustained digestion of spinal cord injury scar tissue.
Combining <scp>CD34</scp>+ stem cell selection with prophylactic pathogen and leukemia directed T‐cell immunotherapy to simultaneously reduce graft versus host disease, infection, and leukemia recurrence after allogeneic stem cell transplant
Authors: David J. Gottlieb, Gaurav Sutrave, Wei Jiang, Selmir Avdic, Janine A. Street, Renee Simms, Leighton E. Clancy, Vicki Antonenas, Brian S. Gloss, Caroline Bateman, David C. Bishop, Kenneth P. Micklethwaite, Emily Blyth
Journal: American Journal of Hematology (2022)

We designed a trial to simultaneously address the problems of graft versus host disease (GVHD), infection, and recurrence of malignancy after allogeneic stem cell transplantation. CD34
A Rare Widespread Cutaneous Langerhans Cell Histiocytosis Manifested on 18F-FDG PET/CT
Authors: Lijuan Wang, Yin Zhang, Hubing Wu
Journal: Clinical Nuclear Medicine (2022)

Widespread cutaneous involvement of Langerhans cell histiocytosis is rare. Here, we report the case of a patient with cutaneous Langerhans cell histiocytosis, which showed a large number of small high 18 F-FDG-avid foci all over the body skin on PET/CT, accompanied with involved lymph nodes in bilateral axillas.
Liver injury after SARS‐CoV‐2 vaccination: Features of immune‐mediated hepatitis, role of corticosteroid therapy and outcome
Authors: Cumali Efe, Anand V. Kulkarni, Benedetta Terziroli Beretta‐Piccoli, Bianca Magro, Albert Stättermayer, Mustafa Cengiz, Daniel Clayton‐Chubb, Craig Lammert, Christine Bernsmeier, Özlem Gül, Fatima Higuera‐de la Tijera, Margarita Anders, Ellina Lytvyak, Mete Akın, Tugrul Purnak, Rodrigo Liberal, Mirta Peralta, Berat Ebik, Serkan Duman, Nurhan Demir, Yasemin Balaban, Álvaro Urzua, Fernando Contreras, Maria Grazia Venturelli, Yılmaz Bilgiç, Adriana Medina, Marcos Girala, Fulya Günşar, Maria‐Carlota Londoño, Theodoros Androutsakos, Ayelen Kisch, Alper Yurci, Fatih Güzelbulut, Yasir Furkan Çağın, Enver Avcı, Murat Akyıldız, Emine Kübra Dindar‐Demiray, Murat Harputluoğlu, Rahul Kumar, Sanjaya K. Satapathy, Manuel Mendizabal, Marcelo Silva, Stefano Fagiuoli, Stuart K. Roberts, Neşe Karadağ Soylu, Ramazan Idilman, Eric M. Yoshida, Aldo J. Montano‐Loza, George N. Dalekos, Ezequiel Ridruejo, Thomas D. Schiano, Staffan Wahlin
Journal: Hepatology (2022)

A few case reports of autoimmune hepatitis-like liver injury have been reported after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination. We evaluated clinical features, treatment response and outcomes of liver injury following SARS-CoV-2 vaccination in a large case series.We collected data from cases in 18 countries. The type of liver injury was assessed with the R-value. The study population was categorized according to features of immune-mediated hepatitis (positive autoantibodies and elevated immunoglobulin G levels) and corticosteroid therapy for the liver injury. We identified 87 patients (63%, female), median age 48 (range: 18-79) years at presentation. Liver injury was diagnosed a median 15 (range: 3-65) days after vaccination. Fifty-one cases (59%) were attributed to the Pfizer-BioNTech (BNT162b2) vaccine, 20 (23%) cases to the Oxford-AstraZeneca (ChAdOX1 nCoV-19) vaccine and 16 (18%) cases to the Moderna (mRNA-1273) vaccine. The liver injury was predominantly hepatocellular (84%) and 57% of patients showed features of immune-mediated hepatitis. Corticosteroids were given to 46 (53%) patients, more often for grade 3-4 liver injury than for grade 1-2 liver injury (88.9% vs. 43.5%, p = 0.001) and more often for patients with than without immune-mediated hepatitis (71.1% vs. 38.2%, p = 0.003). All patients showed resolution of liver injury except for one man (1.1%) who developed liver failure and underwent liver transplantation. Steroid therapy was withdrawn during the observation period in 12 (26%) patients after complete biochemical resolution. None had a relapse during follow-up.SARS-CoV-2 vaccination can be associated with liver injury. Corticosteroid therapy may be beneficial in those with immune-mediated features or severe hepatitis. Outcome was generally favorable, but vaccine-associated liver injury led to fulminant liver failure in one patient.
JAMA Cardiology
Authors: Patrick O'gara, Marc Sabatine, Clyde Boston, Ann Yancy, Michael Pencina, Carolina North, Robert Harrington, Adrian Hernandez, Mhs Durham, North Carolina, Ajay Kirtane, New York, Roxana Mehran, Pradeep Natarajan, Kristen Boston, Seattle Patton, Washington Turakhia, James Udelson, Sadiya Khan, Gregg Fonarow, Los Angeles, Sharlene Day, Laine Thomas, Akhil Narang, Julia Getts, Eugene Braunwald, Judith Hochman, Donald Lloyd-Jones, Scm Chicago, Michael Parmacek, Daniel Simon, Sidney Smith, Chapel Hill, Carolina Douglas, E Vaughan, Myron Weisfeldt, Maryland Douglas, P Zipes, Paul Armstrong, Shinya Goto, Peter Liu, Renato Lopes, Carolina Prabhakaran, Hugh Watkins, Harvey White, Habib Yacoub, Frs London, Phil Fontanarosa, Annette Flanagin, Robert Golub, Michael Berkwits, Brenda Gregoline, Tracy Frey, Iris Lo, Kevin Brown, Bernadette Hromin, Erin Keenan, Rebecca Langley, Kris Simmons, Connie Manno, Sara Billings, Doug Brandt, Timothy Gray, Peter Olson, Juliet Orellana, Paul Ruich, Kirby Snell, Judith Ahlers, Stephanie Beckmeyer, Dawn Bielawski, Jane Calayag, Jan Clavey, Mary Coerver-Connolly, Amy Eutsey, Paul Jaworski, Ruth Kaufman, Laura King, Julia Kurtz, Martha Lentz, Donna Lysak, Jenny Mackay, Charon Pierson, Lori Ryan, Thressa Smith, Annette Theuring, Donna Thordsen, Christine Tilles, Suzanne Walker, Cara Wallace, Becki Weiss, Christina West, Caroline Woods, Larry Bryant, Jacob Kendall-Taylor, Monica Mungle, Lenette Gardner-Gullens, Fanny Brown, Anna Bukowski, Lee Calibeo, Tosca Hall, Erin Kato, Rachell Lozano, Kenneth Otani, Caroline Sietmann, Angelia Waltower, Jesse Mcquarters, Elena Guobyte, Emily Ling, Daniel Morrow, Shelly Steff, Deanna Bellandi, Jim Michalski, Eman Aly, Reuben Rios, Mary Ferkaluk, Jonathan Laxamana, Sidra Bonner, Heather Hsu, Andrew Ibrahim, Karen Bucher, Andy Rekito, Nick Reback, Lohitha Kethu, Marla Erson, Joseph Thornton, Thomas Easley, Brian Shields, Karen Adams-Taylor, Paul Gee, Monica Smith, Julie Burton, Ronna Hewitt, Mary Sieck, Geneine Someren, Jamaal Vargas, Content Systems, Mike Bujewski, Nathan Mitre, Digital Production, Regina Brownlee, Amanda Camino, Brenda Chandler-Grayer, Emily Dunn, Amy Evers, Maleeka Holden, Teri Hutchison, Dan Knowles, Joshua Lampinen, Natalie Marsh, Patricia Panek, Marla Seidell, La Son, Diggs Sledge, Julian Graphics, Joe Amft, Jonathan Chala, James Collver, Maria Duda, Fred Furtner, Carolyn Hall, Maria Kowalkowski, Joy Farrell, Maria Giannini, Sasha Grossman, Kate Lander, Judith Literskis, Teresa Omiotek, Michael Ryder, James Madara, Robert Bonow
Journal: JAMA Cardiology (2022)

science, is a leading editorial priority.
Sustainability of a Clinical Decision Support Intervention for Outpatient Care for Emergency Department Patients With Acute Pulmonary Embolism
Authors: David R. Vinson, Scott D. Casey, Peter L. Vuong, Jie Huang, Dustin W. Ballard, Mary E. Reed
Journal: JAMA Network Open (2022)

Physicians commonly hospitalize patients presenting to the emergency department (ED) with acute pulmonary embolism (PE), despite eligibility for safe outpatient management. Risk stratification using electronic health record-embedded clinical decision support systems can aid physician site-of-care decision-making and increase safe outpatient management. The long-term sustainability of early improvements after the cessation of trial-based, champion-led promotion is uncertain.To evaluate the sustainability of recommended site-of-care decision-making support 4 years after initial physician champion-led interventions to increase outpatient management for patients with acute PE.This retrospective cohort study was conducted in 21 US community hospitals in an integrated health system. Participants included adult patients presenting to the ED with acute PE. Study sites had participated in an original decision-support intervention trial 4 years prior to the current study period: 10 sites were intervention sites, 11 sites were controls. In that trial, decision support with champion promotion resulted in significantly higher outpatient management at intervention sites compared with controls. After trial completion, all study sites were given continued access to a modified decision-support tool without further champion-led outreach. Data were analyzed from January 2019 to February 2020.ED treatment with a modified clinical decision support tool.The main outcome was frequency of outpatient management, defined as discharge home directly from the ED, stratified by the PE Severity Index. The safety measure of outpatient care was 7-day PE-related hospitalization.This study included 1039 patients, including 533 (51.3%) women, with a median (IQR) age of 65 (52-74) years. Nearly half (474 patients [45.6%]) were rated lower risk on the PE Severity Index. Overall, 278 patients (26.8%) were treated as outpatients, with only four 7-day PE-related hospitalizations (1.4%; 95% CI, 0.4%-3.6%). The practice gap in outpatient management created by the earlier trial persisted in the outpatient management for patients with lower risk: 109 of 236 patients (46.2%) at former intervention sites vs 81 of 238 patients (34.0%) at former control sites (difference, 12.2; [95% CI, 3.4-20.9] percentage points; P = .007), with wide interfacility variation (range, 7.1%-47.1%).In this cohort study, a champion-led, decision-support intervention to increase outpatient management for patients presenting to the ED with acute pulmonary embolism was associated with sustained higher rates of outpatient management 4 years later. The application of our findings to improving sustainability of practice change for other clinical conditions warrants further study.